After add/remove explicit hydrogens 3D structure become a 2D

**Steps to Reproduce**
1. Add in Micro mode from Structure Library 3D structure `C20H20`
2. Press add/remove explicit hydrogens 2 times
3. Press 3D Viewer button and look on structure

**Actual behavior**
After add/remove explicit hydrogens 3D structure become a 2D

**Expected behavior**
After add/remove explicit hydrogens 3D structure not become a 2D

**Screenshots**

https://github.com/user-attachments/assets/65399367-27a9-432f-8ee2-042bfec8aa4f

**Desktop:**
- OS: Windows 11
- Browser Chrome
- Version 128.0.6613.120 (Official Build) (64-bit)

**Ketcher version**
[Version 2.26.0-rc.6]
**Indigo version**
[Version 1.25.0-rc.4]

**Description provided by the user:**
### Remove explicit hydrogens Structure error after switching

if the original structure is 3D structure, I now switch more than 3 times, the original structure has changed, the 3D structure should have become 2D

### **MOL Struct It's in 3D struct**
```

Ketcher 10302411 12D 1 1.00000 0.00000 0

40 50 0 0 0 0 0 0 0 0999 V2000
13.1532 -7.7757 -2.7155 H 0 0 0 0 0 0 0 0 0 0 0 0
14.6565 -6.2596 -2.7886 H 0 0 0 0 0 0 0 0 0 0 0 0
14.6090 -6.7985 -1.6168 C 0 0 0 0 0 0 0 0 0 0 0 0
14.0744 -4.6859 -1.3386 H 0 0 0 0 0 0 0 0 0 0 0 0
11.7458 -7.2543 -1.3517 H 0 0 0 0 0 0 0 0 0 0 0 0
12.3600 -5.3293 -0.5122 H 0 0 0 0 0 0 0 0 0 0 0 0
12.8458 -7.3637 -0.7224 C 0 0 0 0 0 0 0 0 0 0 0 0
16.6323 -7.1512 -2.0756 H 0 0 0 0 0 0 0 0 0 0 0 0
15.6841 -7.3076 -1.2493 C 0 0 0 0 0 0 0 0 0 0 0 0
16.2892 -9.2211 -1.7447 H 0 0 0 0 0 0 0 0 0 0 0 0
16.6897 -9.6193 0.3837 H 0 0 0 0 0 0 0 0 0 0 0 0
15.6816 -8.6938 0.2368 C 0 0 0 0 0 0 0 0 0 0 0 0
17.1878 -6.2858 -0.3405 H 0 0 0 0 0 0 0 0 0 0 0 0
17.2042 -7.8533 1.1684 H 0 0 0 0 0 0 0 0 0 0 0 0
14.0874 -8.6860 2.7771 H 0 0 0 0 0 0 0 0 0 0 0 0
14.6615 -10.1692 1.3930 H 0 0 0 0 0 0 0 0 0 0 0 0
14.5916 -9.0478 0.7882 C 0 0 0 0 0 0 0 0 0 0 0 0
13.1105 -10.2641 -0.1449 H 0 0 0 0 0 0 0 0 0 0 0 0
12.3462 -7.8837 2.1925 H 0 0 0 0 0 0 0 0 0 0 0 0
11.7750 -8.8886 0.3668 H 0 0 0 0 0 0 0 0 0 0 0 0
12.8377 -8.2264 0.1912 C 0 0 0 0 0 0 0 0 0 0 0 0
13.1768 -7.6569 1.2757 C 0 0 0 0 0 0 0 0 0 0 0 0
15.6797 -4.7406 0.1368 H 0 0 0 0 0 0 0 0 0 0 0 0
16.0235 -6.7554 -0.1611 C 0 0 0 0 0 0 0 0 0 0 0 0
14.2615 -5.9270 -0.7658 C 0 0 0 0 0 0 0 0 0 0 0 0
14.2641 -8.1721 1.6401 C 0 0 0 0 0 0 0 0 0 0 0 0
16.0201 -7.6183 0.7433 C 0 0 0 0 0 0 0 0 0 0 0 0
15.6962 -7.1587 2.6832 H 0 0 0 0 0 0 0 0 0 0 0 0
13.1839 -6.2715 -0.2167 C 0 0 0 0 0 0 0 0 0 0 0 0
12.7054 -5.5937 1.6150 H 0 0 0 0 0 0 0 0 0 0 0 0
14.5922 -6.2301 1.2227 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7179 -5.3154 2.0918 H 0 0 0 0 0 0 0 0 0 0 0 0
15.1298 -7.2887 1.6098 C 0 0 0 0 0 0 0 0 0 0 0 0
13.3796 -6.4589 1.0143 C 0 0 0 0 0 0 0 0 0 0 0 0
15.1472 -5.8952 0.1110 C 0 0 0 0 0 0 0 0 0 0 0 0
14.2617 -8.7454 -1.1975 C 0 0 0 0 0 0 0 0 0 0 0 0
13.7131 -9.0816 -0.0953 C 0 0 0 0 0 0 0 0 0 0 0 0
15.4798 -8.5079 -0.9871 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1480 -9.5883 -2.0352 H 0 0 0 0 0 0 0 0 0 0 0 0
13.7296 -7.6781 -1.5827 C 0 0 0 0 0 0 0 0 0 0 0 0
1 40 1 0 0 0 0
2 3 1 0 0 0 0
3 9 1 0 0 0 0
3 25 1 0 0 0 0
3 40 1 0 0 0 0
4 25 1 0 0 0 0
5 7 1 0 0 0 0
6 29 1 0 0 0 0
7 21 1 0 0 0 0
7 29 1 0 0 0 0
7 40 1 0 0 0 0
8 9 1 0 0 0 0
9 24 1 0 0 0 0
9 38 1 0 0 0 0
10 38 1 0 0 0 0
11 12 1 0 0 0 0
12 17 1 0 0 0 0
12 27 1 0 0 0 0
12 38 1 0 0 0 0
13 24 1 0 0 0 0
14 27 1 0 0 0 0
15 26 1 0 0 0 0
16 17 1 0 0 0 0
17 26 1 0 0 0 0
17 37 1 0 0 0 0
18 37 1 0 0 0 0
19 22 1 0 0 0 0
20 21 1 0 0 0 0
21 22 1 0 0 0 0
21 37 1 0 0 0 0
22 26 1 0 0 0 0
22 34 1 0 0 0 0
23 35 1 0 0 0 0
24 27 1 0 0 0 0
24 35 1 0 0 0 0
25 29 1 0 0 0 0
25 35 1 0 0 0 0
26 33 1 0 0 0 0
27 33 1 0 0 0 0
28 33 1 0 0 0 0
29 34 1 0 0 0 0
30 34 1 0 0 0 0
31 32 1 0 0 0 0
31 33 1 0 0 0 0
31 35 1 0 0 0 0
36 37 1 0 0 0 0
36 38 1 0 0 0 0
36 39 1 0 0 0 0
36 40 1 0 0 0 0
31 34 1 0 0 0 0
M END

```

### **This is initial**

### **Click the button three times**

### **At this point the 3D structure also disappeared and the preview 3D became 2D**